Referenced by Tensor::add(), HemeBindingMover::apply(), protocols::moves::SimpleCstMover::apply(), apply_all_frags(), apply_mask(), aro_pack_output(), aro_pack_pdbstats_from_pose(), auto-DRRAFTER_setup::auto_setup_helices(), base_pair_to_base_pair_test(), build_next_nucleotide_test(), calc_dihedral_rms(), calc_median(), calc_RMSE(), calculate_percent_disorder(), calculate_theoretical_RNA_length(), center_of_mass(), center_pose_at_origin(), ch_o_pdbstats_from_pose(), Tensor::check(), checkresiduecount(), color_by_lj_test(), compare_gpu_result_against_cpu(), containment_and_clash_checks(), correct_dunbrack(), correct_rama(), detail::iterator_buffer< OutputIt, T, Traits >::count(), count_backbone_atoms(), detail::count_digits(), count_numerically(), basic::resource_manager::ResourceManager::deallocate_resource(), define_states_test(), dinucleotide_test(), do_event_prediction(), dock(), TCDock::dump_top_hits(), ensure_cyclic(), basic::execute(), expand_chi_for_silent_structs(), fa_cenpack_pdbstats_from_pose(), files_for_openMM_test(), for(), formatter< std::tm, Char >::format(), utility::io::icstream::get(), utility::io::izstream::get(), get_atom_packing_score(), basic::citation_manager::CitationCollection::get_citations_formatted(), MatchSet::get_contacting_stub(), get_info_test(), get_localbfacs(), numeric::MathNTensor< T, N >::get_mathmatrix(), utility::get_resnum_and_chain_from_one_tag(), get_sc_bfactor(), get_sc_rmsd(), get_sidechain_rmsd(), get_three_atom_sc_rmsd(), utility::io::icstream::getline(), utility::io::izstream::getline(), gpu_score_test(), utility::io::icstream::ignore(), utility::io::izstream::ignore(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), numeric::random::mt19937_RG::init_by_array(), input_subset_poses(), TCDock::justone(), load_loops_from_file(), main(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::maybe_default_constructible(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >::maybe_has_equal_operator(), measure_disorder(), mg_pdbstats_from_pose(), mg_pdbstats_test(), numeric::linear_algebra::minimum_bounding_ellipse(), modeler_closure_test(), modeler_map_test(), apps::pilot::MultiTemplateAlignChunkMover::MultiTemplateAlignChunkMover(), natoms(), numeric::geometry::hashing::xyzStripeHash::nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::nbcount(), numeric::geometry::hashing::xyzStripeHash::nbcount_raw(), normalize_info(), nsat(), nucleobase_probe_score_test(), num_trimer_contacts(), one_chain_MC_sampling(), one_chain_ST_MC(), output_benchmark_stuff(), output_constraints_for_full_length(), output_local_minima(), output_packstat_pdb(), output_to_silent(), parse_into_stub(), parse_ss_regions(), SphereSample::pdb_from_level(), polar_pdbstats_from_pose(), polar_pdbstats_test(), pose_cbcount(), PoseWrap::PoseWrap(), predict_chem_map_test(), numeric::expression_parser::TokenSet::print_to_curr_pos(), processChildren(), processChildrenIntensification(), proline_rama_pdbstats_from_pose(), utility::io::icstream::read(), utility::io::izstream::read(), read_B_vals(), read_complex_type(), read_fragdata(), utility::io::icstream::readsome(), utility::io::izstream::readsome(), rebuild_centroid_test(), recenter_with_missing(), rg2d(), rhiju_pdbstats(), rna_fullatom_multiscore_test(), rna_stack_pdbstats_from_pose(), run(), TCDock::run(), core::pack::annealer::FixbbSimAnnealer::run(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), safe_duration_cast::safe_duration_cast(), sample_new_base_in_two_base_pair_pose(), sample_trp_test(), sample_trp_tyr_test(), score12_plot_test(), search_other_atoms(), search_translations(), set_secstruct_from_psipred_ss2(), setup_alignment_map(), setup_mask(), setup_pose(), setup_rhiju_fold_tree(), sicdock_thread_num(), simulate_ERMS(), basic::datacache::ConstDataMap::size(), spinner_test(), numeric::interpolation::spline_from_file(), stepwise_template_test(), detail::strftime(), Tensor::sum_to(), svm_check_parameter(), svm_cross_validation(), svm_group_classes(), svm_svr_probability(), svm_train(), sweep_params_from_match_constraint_file(), FunctorTest::test_basic(), FunctorTest::test_functor_async_sequence(), FunctorTest::test_functor_sequence(), test_k_square(), zlib_stream::basic_unzip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::unzip_from_stream(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::write(), zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::write(), utility::io::ocstream::write(), utility::io::ozstream::write(), protocols::moves::SimpleCstMover::write(), and write_cluster_frags().
